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NCBI C++ ToolKit: src/objtools/validator/huge_file_validator.cpp Source File

& molInfo = pSeqdesc->GetMolinfo();

(molInfo.IsSetTech() &&

(

pId :

.m_ids) {

(

pId : ids) {

(pId && pId->IsOther() && pId->GetOther().IsSetAccession()) {

(

pId :

.m_ids) {

(pId && pId->IsOther() && pId->GetOther().IsSetAccession()) {

(

pId :

.m_ids) {

& molInfo = pSeqdesc->

();

(

pId :

.m_ids) {

list<CRef<CSeq_id>> tmpIds;

(

pId : ids) {

pTmpId->Assign(*pId);

tmpIds.push_back(pTmpId);

& message,

m_Options(options) {}

& biosets =

.GetBiosets();

(biosets.size() < 2) {

it =

(biosets.begin());

suppressContext =

;

(

.FindBioseq(pId) !=

);

(

: collidingNumbers) {

(! (

.GetSubmitBlock())) {

(! (

.GetSubmitBlock())) {

,

,

(

pSetClass =

.GetTopLevelClass();

,

(

.GetBiosets().size() < 2) {

.PreprocessHugeFile =

;

(

.IsNotJustLocalOrGeneral()) {

.NotJustLocalOrGeneral =

;

(

pPub : pub.

().

()) {

}

(pPub->IsGen()) {

&

= pPub->GetGen();

(

.IsSetSerial_number()) {

.GetTypeInfo()->DefaultReadData(

, pMolInfo);

* pObject =

.GetObjectPtr();

.GetTypeInfo()->DefaultReadData(

, pObject);

.GetTypeInfo()->DefaultReadData(

, pPubdesc);

* pObject =

.GetObjectPtr();

.GetTypeInfo()->DefaultReadData(

, pObject);

.GetTypeInfo()->DefaultSkipData(

);

.GetTypeInfo()->DefaultReadData(

,

.GetObjectPtr());

* pObject =

.GetObjectPtr();

.GetTypeInfo()->DefaultReadData(

, pObject);

(pUser_object->IsSetType() && pUser_object->GetType().IsStr() &&

(pUser_object->GetType().GetStr(),

)) {

.GetTypeInfo()->DefaultReadData(

, pSeqhist);

(pSeqhist->IsSetAssembly() && ! pSeqhist->GetAssembly().empty()) {

.GetTypeInfo()->DefaultSkipData(

);

gbqual_qual_mi = gbqual_info.FindMember(

);

.GetTypeInfo()->DefaultReadData(

, &

);

(

==

) {

& hugeSetId,

(biosets.size() < 2 || bioseqs.size() < 1) {

(

it =

(biosets.begin());

& firstBioseq = bioseqs.begin();

& parentIt = firstBioseq->m_parent_set;

(

it = firstBioseq; it != bioseqs.end(); ++it) {

(

(it->m_mol) && it->m_parent_set == parentIt) {

& hugeSetId,

(

pErrorItem : pErrors->GetErrs()) {

pPrunedErrors->AddValidErrItem(pErrorItem);

pErrors = pPrunedErrors;

& hugeSetId,

[globalInfo, hugeSetId](

pItem) { return pItem.Empty() || s_DropErrorItem(globalInfo, hugeSetId, *pItem); });

errors.erase(it, errors.end());

User-defined methods of the data storage class.

@ eErr_SEQ_DESCR_InconsistentBioSources_ConLocation

@ eErr_GENERIC_MissingPubRequirement

@ eErr_SEQ_DESCR_NoOrgFound

@ eErr_SEQ_DESCR_TransgenicProblem

@ eErr_SEQ_PKG_InconsistentMoltypeSet

@ eErr_SEQ_DESCR_NoPubFound

@ eErr_SEQ_INST_MitoMetazoanTooLong

@ eErr_SEQ_DESCR_NoSourceDescriptor

@ eErr_GENERIC_CollidingSerialNumbers

@ eErr_SEQ_FEAT_OnlyGeneXrefs

@ eErr_SEQ_FEAT_TooManyInferenceAccessions

@ eErr_SEQ_INST_TpaAssemblyProblem

User-defined methods of the data storage class.

void remove_if(Container &c, Predicate *__pred)

CConstRef< CSeqdesc > GetClosestDescriptor(const TBioseqInfo &info, CSeqdesc::E_Choice choice) const

auto & GetBiosets() const

static bool IsHugeSet(CBioseq_set::TClass setClass)

auto & GetBioseqs() const

const CBioseq_set::TClass * GetTopLevelClass() const

void ReportGlobalErrors(const TGlobalInfo &globalInfo, IValidError &errors) const

void x_ReportConflictingBiomols(IValidError &errors) const

void x_ReportMissingCitSubs(bool hasRefSeqAccession, IValidError &errors) const

unique_ptr< string > m_pIdString

void UpdateValidatorContext(TGlobalInfo &globalInfo, SValidatorContext &context) const

string x_GetIdString() const

void x_PostMsg(EDiagSev severity, EErrType errorType, const string &message, IValidError &errors) const

edit::CHugeAsnReader TReader

string x_GetHugeSetLabel() const

CHugeFileValidator(const TReader &reader, TOptions options)

void x_ReportMissingBioSources(IValidError &errors) const

void x_ReportCollidingSerialNumbers(const set< int > &collidingNumbers, IValidError &errors) const

void x_ReportMissingPubs(IValidError &errors) const

static void RegisterReaderHooks(CObjectIStream &objStream, SGlobalInfo &m_GlobalInfo)

void ReportPostErrors(const SValidatorContext &context, IValidError &errors) const

bool IsInBlob(const CSeq_id &id) const

@Pubdesc.hpp User-defined methods of the data storage class.

static string GetBioseqSetLabel(const CBioseq_set &st, CRef< CScope > scope, bool suppress_context)

static bool IsTSAAccession(const CSeq_id &id)

static bool IsWGSAccession(const CSeq_id &id)

@ eVal_refseq_conventions

virtual void AddValidErrItem(EDiagSev sev, unsigned int ec, const string &msg, const string &desc, const CSerialObject &obj, const string &acc, const int ver, const string &location=kEmptyStr, const int seq_offset=0)=0

iterator_bool insert(const value_type &val)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static const char * str(char *buf, int n)

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

static const TObjectType * SafeCast(TTypeInfo type)

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static const char label[]

bool IsSet(void) const

Check if a value has been assigned to data member.

const Tdata & Get(void) const

Get the member data.

@ e_Gi

GenInfo Integrated Database.

@ eClass_wgs_set

whole genome shotgun project

@ eClass_nuc_prot

nuc acid and coded proteins

@ eClass_gen_prod_set

genomic products, chrom+mRNA+protein

bool IsSetBiomol(void) const

Check if a value has been assigned to Biomol data member.

TBiomol GetBiomol(void) const

Get the Biomol member data.

EMol

molecule class in living organism

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

const TPub & GetPub(void) const

Get the Pub member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ eRepr_virtual

no seq data

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ e_Molinfo

info on the molecule and techniques

@ eMol_na

just a nucleic acid

const TMsg & GetMsg(void) const

Get the Msg member data.

TErrIndex GetErrIndex(void) const

Get the ErrIndex member data.

const TAccession & GetAccession(void) const

Get the Accession member data.

static bool s_IsWGS(const TBioseqInfo &info, const CHugeAsnReader &reader)

static bool s_x_ReportMissingCitSub(const TBioseqInfo &info, const CHugeAsnReader &reader, bool IsRefSeq)

static bool s_IsGpipe(const TBioseqInfo &info)

bool g_IsCuratedRefSeq(const TBioseqInfo &info)

static bool s_IsMaster(const TBioseqInfo &info)

static string s_GetBioseqAcc(const CSeq_id &id, int *version)

static bool s_IsNa(CSeq_inst::EMol mol)

static bool s_CuratedRefSeq(const string &accession)

static bool s_IsTSAContig(const TBioseqInfo &info, const CHugeAsnReader &reader)

static bool s_IsNoncuratedRefSeq(const list< CConstRef< CSeq_id >> &ids)

static bool s_x_ReportMissingPubs(const TBioseqInfo &info, const CHugeAsnReader &reader)

static void s_UpdateGlobalInfo(const CPubdesc &pub, CHugeFileValidator::TGlobalInfo &globalInfo)

static bool s_DropErrorItem(const CHugeFileValidator::TGlobalInfo &globalInfo, const string &hugeSetId, const CValidErrItem &item)

static string s_GetIdString(const list< CConstRef< CSeq_id >> &ids, int *version)

static bool s_IsWGSMaster(const TBioseqInfo &info, const CHugeAsnReader &reader)

string g_GetHugeSetIdString(const CHugeAsnReader &reader)

void g_PostprocessErrors(const CHugeFileValidator::TGlobalInfo &globalInfo, const string &hugeSetId, CRef< CValidError > &pErrors)

const string version

version string

std::istream & in(std::istream &in_, double &x_)

void SetLocalSkipHook(const CObjectTypeInfo &obj_type_info, CObjectIStream &istr, _Func _func)

void SetLocalReadHook(const CObjectTypeInfo &obj_type_info, CObjectIStream &ostr, _Func _func)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

set< int > pubSerialNumbers

set< CMolInfo::TBiomol > biomols

int CumulativeInferenceCount

set< int > conflictingSerialNumbers

const int InferenceAccessionCutoff

static CS_CONTEXT * context

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